Annotation of environmental OMICS data: application to the transcriptomics domain.

Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.

Exposure to 2,4-decadienal negatively impacts upon marine invertebrate larval fitness.

Diatoms liberate volatile, biologically active unsaturated aldehydes following cell damage, which negatively impact upon invertebrate reproductive processes such as fertilization, embryogenesis and larval survival. 2,4-Decadienal is frequently identified among the aldehydes produced and is one of the more biologically active. The majority of studies which have examined the toxic effects of diatom aldehydes to invertebrate reproduction have scored egg production and/or hatching success as indicators of biological impacts. There are very few studies which have dealt specifically with the impacts of diatom-derived aldehydes on larval fitness. Larval stages of the polychaetes Arenicola marina and Nereis virens and the echinoderms Asterias rubens and Psammechinus miliaris exposed to 2,4-decadienal at sub 1 microg ml(-1) concentrations suffered reduced survival over the incubation period (day 1-8 post fertilization) with detectable differences for the polychates at a concentration of 0.005 and 0.01-0.1 microg ml(-1) for the echinoderms. Susceptibility of larval N. virens was investigated using stage specific 24 h exposures at 2,4-decadienal concentrations up to 1.5 microg ml(-1). A clear stage specific effect was found, with earlier larval stages most vulnerable. Nectochaete larvae (9-10 d) showed no reduction in survival at the concentrations assayed. Fluctuating asymmetry (FA), defined as random deviations from perfect bilateral symmetry, was used to analyse fitness of larval P. miliaris exposed to 2,4-decadienal at concentrations of 0.1, 0.5 and 1 microg ml(-1). The degree and frequency of asymmetrical development increased with increasing 2,4-decadienal concentration. Equally, as FA increased larval survival decreased. These results provide further support for the teratogenic nature of 2,4-decadienal and its negative impact on invertebrate larval fitness.

Clock gene evolution and functional divergence.

In considering the impact of the earth's changing geophysical conditions during the history of life, it is surprising to learn that the earth's rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the "protoclock" in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.

Isotope trophic-step fractionation: a dynamic equilibrium model.

Trophic position is a fundamental feature of food-web structure, knowledge of which is being improved by stable isotope approaches which assume a constant enrichment in heavier isotopes in consumers relative to their diet. We argue that the typical enrichment reflects a dynamic equilibrium between fractionation vectors associated with assimilation and excretion. We develop a linear model to characterize the relationship between the equilibrium isotopic signature and the feeding rate influenced by isotopic discrimination during assimilation and excretion. We present new data for both diet switching and starvation experiments using a marine worm Nereis virens and use this, and previously published data for a fish, bird and mammal to calculate controlling parameters from observations of the isotopic signature following diet-switching and the onset of starvation. We show that the observed variance in isotopic signatures at each trophic step carries substantially more information than has been used hitherto and is influenced by feeding rate in addition to the isotopic signature of the food source. Using the linear model as a tool we predict that parasitic organisms may be depleted relative to the tissues of their host.

The use of a brine shrimp (Artemia salina) bioassay to assess the toxicity of diatom extracts and short chain aldehydes.

Water soluble algal extracts, the aldehydes 2E,4E-decadienal, decanal, undecanal and the fatty acid eicosapentaenoic acid (EPA) were assayed for toxicity to hatching success and larval mortality of the brine shrimp Artemia salina. Both crude cellular extracts of the diatoms Skeletonema costatum and Nitzschia commutata and the diatom-derived short chain aldehyde decadienal were found to inhibit hatching success of A. salina cysts in a dose-dependent manner. Decadienal also significantly affected larval mortality rates in 24 and 72 h exposure incubations. The Artemia hatching success assay was the least sensitive of the three (EC50=3.94 microg ml(-1)). A greater sensitivity was observed for the 72 h compared with the 24 h exposure trials (EC50 for 24h=2.14, 72 h=0.023 microg ml(-1)). Decanal did not significantly affect survival or hatching success at the concentrations tested. Undecanal and EPA showed a limited toxic effect in naupliar mortality trials. We suggest that 72 h Artemia exposure trials represent an acceptable bioassay for diatom toxicity where alternative bioassays are unavailable.

Inhibition of embryonic development and fertilization in broadcast spawning marine invertebrates by water soluble diatom extracts and the diatom toxin 2-trans,4-trans decadienal.

Water soluble diatom extracts and the diatom aldehyde 2-trans,4-trans decadienal were assayed on the gametes and embryos of the broadcast spawning polychaetes Arenicola marina and Nereis virens and the echinoderms Asterias rubens and Psammechinus miliaris. Both crude cellular extracts and purified aldehyde were found to inhibit fertilization, embryogenesis and hatching success in a dose dependent manner. Intact diatom cells had no discernable effect on fertilization or development. Extracts of Skeletonema costatum were generally more effective than Nitzschia commutata in inhibiting development and fertilization. There was considerable interspecific variation in terms of toxin sensitivity. The polychaetes were more sensitive to the effects than the echinoderms. Within the polychaetes A. marina was the more tolerant in terms of developmental competence but N. virens had a higher fertilization rate. Echinoid embryos were more tolerant than asteroid embryos. This is the first study to present data on the inhibition of fertilization success by diatom extracts and aldehydes. Our observations are discussed in relation to temporal patterns in spawning and possible adaptive mechanisms to avoid diatom toxicity.

Interaction between photoperiod and an endogenous seasonal factor in influencing the diel locomotor activity of the benthic polychaete Nereis virens Sars.

The locomotor activity of Nereis virens Sars associated with food prospecting was investigated in response to photoperiod and season using an actograph. Experimental animals which had been reared under natural photoperiods were exposed to two constant photoperiodic treatments, LD 16:8 and LD 8:16, in both the autumn and winter and in the absence of tidal entrainment. Autocorrelation analysis of rhythmicity showed that during the autumn, animals under the LD 16:8 photoperiod displayed a strong nocturnal rhythm of activity, whereas animals under the LD 8:16 photoperiod showed only a weak nocturnal activity rhythm. This is believed to represent an autumn feeding cessation that is triggered when the animals pass through a critical photoperiod LD(crit) <12:>12. Later in the winter, however, animals exposed to both photoperiodic treatments showed strong rhythms of foraging activity irrespective of the imposed photoperiod. It is suggested that the autumn cessation may maximize the fitness of N. virens, a spring-breeding semelparous organism, by reducing risk during gamete maturation, while spontaneous resurgence of activity after the winter solstice permits animals that are not physiologically competent to spawn to accrue further metabolic reserves. This response is believed to be initiated by a seasonal (possibly circannual) endogenous oscillator or interval timer.

Tidal, daily, and lunar-day activity cycles in the marine polychaete Nereis virens.

The burrow emergence activity of the wild caught ragworm Nereis virens Sars associated with food prospecting was investigated under various photoperiodic (LD) and simulated tidal cycles (STC) using a laboratory based actograph. Just over half (57%) of the animals under LD with STC displayed significant tidal (approximately 12.4 h) and/or lunar-day (approximately 24.8 h) activity patterns. Under constant light (LL) plus a STC, 25% of all animals were tidal, while one animal responded with a circadian (24.2 h) activity rhythm suggestive of cross-modal entrainment where the environmental stimulus of one period entrains rhythmic behavior of a different period. All peaks of activity under a STC, apart from that of the individual cross-modal entrainment case, coincided with the period of tank flooding. Under only LD without a STC, 49% of the animals showed nocturnal (approximately 24 h) activity. When animals were maintained under free-running LL conditions, 15% displayed significant rhythmicity with circatidal and circadian/circalunidian periodicities. Although activity cycles in N. virens at the population level are robust, at the individual level they are particularly labile, suggesting complex biological clock-control with multiple clock output pathways.